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diff --git a/ds9/doc/faq.html b/ds9/doc/faq.html index 9644071..3e4ab82 100644 --- a/ds9/doc/faq.html +++ b/ds9/doc/faq.html @@ -1,818 +1,707 @@ -<!DOCTYPE doctype PUBLIC "-//w3c//dtd html 4.0 transitional//en"> +<!DOCTYPE doctype PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> <html> - <head> - <meta http-equiv="Content-Type" content="text/html; - charset=windows-1252"> - <meta name="GENERATOR" content="Mozilla/4.78 [en] (X11; U; Linux - 2.4.7-10 i686) [Netscape]"> - <title>DS9 FAQ</title> - </head> - <body vlink="#551a8b" text="#000000" link="#0000ee" bgcolor="#ffffff" - alink="#ff0000"> - <h3> <img alt="" src="sun.gif" width="100" height="98" - align="middle"> SAOImageDS9 FAQ</h3> - <blockquote> - <p>This FAQ is a new, on going project, and it is far from being - complete. But as common questions on DS9 are received, the FAQ - will be updated. </p> - <p><b>Contents</b></p> - <blockquote><a href="#Copyright">Copyright</a><br> - <a href="#General">General</a><br> - <a href="#Fonts">Fonts</a><br> - <a href="faq.html#Linux">Linux</a> <br> - <a href="faq.html#Windows">Windows</a> <br> - <a href="#MacOSX">MacOSX</a><br> - <a href="faq.html#X11">X11</a> <br> - <a href="#IRAF">IRAF</a> <br> - <a href="#Coordinates">Coordinates</a> <br> - <a href="#Regions">Regions</a> <br> - <a href="#Printing">Printing</a> <br> - <a href="#XPA">XPA</a><br> - <a href="#VO">VO</a><br> - </blockquote> - </blockquote> - <blockquote> - <p> <b><a name="Copyright"></a>Copyright</b></p> - <blockquote> - <p>DS9 is composed of approximately 20 open source packages, all - of which are distributed under their own open source license - agreements, usually GPL, LGPL, or BSD. In addition, several - open source packages have been developed here at the - Smithsonian Astrophysical Observatory, Cambridge, MA, USA and - are distributed under the terms of the GNU General Public - License as published by the Free Software Foundation. As long - as you continue to adhere to the provisions of the licenses, - you are free to distribute DS9 along with your software.</p> - <p>The <a href="http://www.gnu.org/copyleft/gpl.html">GNU site</a> - contains an excellent FAQ on the the dos and donts of GPL.</p> - </blockquote> - <p><b><a name="General"></a>General</b></p> - <blockquote> - <p><b>The web browser, catalog tool, image server, and other - Analysis functions don't appear to work. Whats going on?<br> - </b></p> - <p>For a number of the Analysis functions, DS9 requires - temporary disk space to download and store data. By default, - this directory is defined by the TMP or TEMP environment - variable. This is usually defined as <tt>/tmp</tt> for Linux - and MacOSX users. For Windows users, this will vary, depending - on which version of Windows you have. In any case, if the temp - directory is not writable, or you have specified an invalid - directory in the preferences, these functions will fail with a - variety of error messages.<br> - </p> - <p><b>My system admin stripped the DS9 binary and now DS9 fails - to start with the following error message:</b></p> - <p><tt>Application initialization failed: Can't find a usable - tk.tcl in the following directories...</tt></p> - <p>DS9 is based on tcl/tk which is a scripting language which - requires many support files. To create a stand alone - application, we <i>fool</i> tcl/tk into thinking that it has - a valid installation. To do this, DS9 is really an - application, along with an zip archive attached. The first - thing DS9 does is to create a virtual file system in memory - and unpack that archive into memory. The application DS9 is - already stripped of debugging symbols when built. </p> - <p>It appears that the <tt>strip</tt> command is <i>stripping</i> - part of the archive, hence DS9 is unable to un-compress it. In - summary, don't <tt>strip</tt> the DS9 binary and everything - works fine. </p> - <p><b>When I open my FITS image, all I see is 'white'. Yet - everything, including the color bar seems to work?</b></p> - <p>New with version 2.1, is support for the DATASEC keyword. - This keyword specifies what portion of the image is valid - data, for calculating min / max and for displaying. This is - very important for images created from CCDs with over scan and - bias strips. By default, this support is enabled. However, a - number of fits images with this keyword, have invalid values. - Therefor, when DS9 opens the image, it finds no valid data to - display. To correct this problem, either disable DATASEC - support, via the Scale menu, or correct the the value of - DATASEC in the fits header. You can also change the default - behavior by disabling DATASEC from the preferences menu.<br> - </p> - </blockquote> - <p> <b><a name="Fonts"></a>Fonts</b></p> - <blockquote> - <p><b>Where is the Symbol Font? How do I enter special - characters into an entry dialog?</b> </p> - <p>The concept of a separate <tt>SYMBOL</tt> font is no longer - implemented with the latest OS font and scripting support, - especially with scalable anti-alias fonts such as Xft for - Linux. Most newer fonts (if not all) now have greek characters - as part of the font. The greek chars start at unicode \u0391 - for 'A' and \u03b1 for 'a'. Each OS has a tool used to build - and copy a string of characters. Then use the Edit:Paste menu - of DS9 to insert the character string.</p> - <p>Linux- Gnome: <b>gucharmap<br> - </b>Linux- KDE: <b>kcharselect<br> - </b>MacOSX: <b>Character Viewer</b> (Select <tt>Edit:Special - Characters</tt>) Now click and drag the characters to a - terminal window. Then select the string and select <tt>Edit:Copy</tt>.<br> - Windows: <b>Character Map</b> (from <tt>Start</tt> button, - select <tt>All Programs</tt>, <tt>Accessories</tt>, <tt>System - - - - - - - Tools</tt> and then <tt>Character Map</tt>)<br> - </p> - </blockquote> - <p> <b><a name="Linux"></a>Linux</b></p> - <blockquote> - <p><b>My /tmp directory is mounted -noexec and bin table - filtering does not work.</b></p> - <p>Set the environment variable FILTER_TMPDIR to a directory - that is both writable and can execute.<br> - </p> - <p><b>I have Red Hat 7, and I'm running KDE. The magnifier keeps - going blank after a few seconds, what's going on?</b> </p> - <p>The problem was in KDE. If the user has decided to hide the - panel taskbar and sets a delay time for when it appears - if the mouse is moved to the panel location, then it - appears that KDE creates mouse events that fool DS9 into - thinking the mouse is outside and it blanks the magnifier. By - turning off the hide panel, the effect goes away. The - alternative is to update to KDE2.1Beta where this method - of dealing with the hidden panel is not used and all is - well, as it was for KDE </p> - <p><b>I have FreeBSD. When I run ds9, I get the following error:</b> - <tt> <b>ELF binary type "0" not known</b> </tt><b>Whats - - - - - - - - going on?</b></p> - <p>The solution was to use the <b><tt>brandelf</tt></b> utility - on the file to ensure that the machine understood that it - was a Linux program.</p> - <p><tt>% brandelf -t Linux (file name)<br> - </tt></p> - <blockquote> </blockquote> - </blockquote> - <p> <b><a name="Windows"></a>Windows</b></p> - <blockquote> - <p><b>When I do Save Image, I get the same result (and this is - true for either .gif, .jpeg, .tiff, .png and .ppm) : it - saves only a stripe at the top of my image.<br> - </b></p> - <p>This problem seems to be caused by running DS9 in Windows XP - compatibility mode. Please un-check the compatibility option - in the properties dialog.<br> - </p> - <p><b>How can I open a FITS file with an extension name?</b></p> - <p><b> </b>By default, the windows port of DS9 uses the Windows - standard dialog box to open and save files. This can be a - problem in that the native Windows dialog will not allow - extensions to the file name, such as <tt>foo.fits[2]</tt>. - You must use the Unix like standard dialogs to be able to - specify an extension. Select <tt>Edit->Preferences->General:Dialogbox</tt> - to change the default standard dialog.</p> - <p><b>Every time I create an auxiliary window in ds9, such as a - Pixel Table, or Analysis Plot, it will retreat behind the - main ds9 window. Then, when I bring the auxiliary window to - the front and move the mouse out of it, it automatically - goes behind the main ds9 window again. What can I do to fix - things so that the auxiliary window stays on top of the ds9 - window?</b> </p> - <p>To fix things so that the auxiliary window stays on top of - the ds9 window, do the following: </p> - <blockquote> - <p><tt>Go to the icon task bar at the bottom of the screen.</tt><tt> - Bring the auxiliary window to the front by clicking on its - icon in the icon task bar.</tt><tt> While the mouse still - is on the aux window icon, press the mouse button, and - keeping it pressed, move the mouse off the task bar.</tt><tt> - Release the mouse while off the task bar.</tt><tt> The - auxiliary window will now stay on top of the main ds9 - window.</tt></p> - <blockquote> </blockquote> - </blockquote> - </blockquote> - <p><b><a name="MacOSX"></a>MacOSX</b><br> - </p> - <blockquote> - <p><b>I can't invoke the 'Save Image' function from the MacOSX - X11 version. I get an error message "An error has occurred - while creating the image. Please make sure entire image is - visible on screen."<br> - </b></p> - Up until MacOSX 10.8 (Mountain Lion), Apple provided their own - version of a X11 server. At first, it was based on XFree86 - (X11R6.6) and available with versions up to MacOSX 10.4. Later - with MacOSX versions 10.5 to 10.7, the Apple's X11 server was - based upon X.org (X11R7.2). <br> - <br> - The Apple version of X11 server for MacOSX 10.5 to 10.7 contains - a bug which fails if you invoke certain X11 calls on a window if - its location is not at 0,0 on the screen. Hence, within DS9, if - you 'Save Image' and your window is not exactly in the upper - left corner, it will fail.<br> - <br> - Again, this only affects users of MacOSX 10.5 to 10.7.<br> - <br> - Starting with MacOSX 10.8, Apple no longer provides a X11 window - server. The user must go to the XQuartz site and - download/install directly. The current version is 2.7.3.<br> - <p><b>When I invoke DS9 MacOSX Aqua from the command line, I get - weird errors such as<tt>:</tt></b></p> - <blockquote> - <p><tt>The document "foo.fits" could not be opened. SAOImage - DS9 cannot open files in the "Flexible Image Transport - System" format.</tt></p> - </blockquote> - <p><b><tt> </tt></b>When opening MacOSX Aqua from the command - line, it is better to use the <tt>OPEN</tt> application as - opposed to specifying the binary directly. The <tt>OPEN</tt> - application sets up the environment just as it is when a user - double clicks.</p> - <tt> # good</tt><br> - <tt>% open /Applications/SAOImage\ DS9.app foo.fits<br> - <br> - # bad<br> - % /Applications/SAOImage\ DS9.app/Contents/MacOS/ds9 bar.fits</tt><br> - <p><b>How can I open a FITS file with an extension name?</b></p> - <p><b> </b>By default, DS9 MacOSX Aqua uses the MacOSX standard - dialog box to open and save files. This can be a problem in - that the native MacOSX dialog will not allow extensions to the - file name, such as <tt>foo.fits[2]</tt>. You must use the - Unix like standard dialogs to be able to specify an extension. - Select <tt>Edit->Preferences->General</tt> to change - the default standard dialog.</p> - <p><b>How do I set my PATH environment variable under MacOSX for - use with external analysis programs, such as funtools?<br> - </b></p> - <p>When you double click on a MacOSX application, it does not - parse any shell startup files, such as ~/.profile. Instead, - the environment is defined using a special environment file, <tt>.MacOSX/environment.plist</tt>. - This file can be created with the MacOSX utility <tt>/Developer/Applications/PropertyListEditor.app. - - - - - - - </tt>For further information, please click <a - href="http://developer.apple.com/qa/qa2001/qa1067.html">here</a>.<br> - </p> - <blockquote> </blockquote> - </blockquote> - <p> <b><a name="X11"></a>X11</b><br> - </p> - <blockquote> - <p><b>Is it possible to work in batch mode without a physical - display?<br> - </b></p> - <p>DS9 is written as an interactive, window client program, and - as a result, does require a window server to be available for - rendering (X11, Windows, or MacOSX).<br> - <br> - Therefore, using DS9 as a batch process can be cumbersome. We - recommend using <tt>xvfb</tt> under X11. Just set up a - virtual display buffer, reset your DISPLAY variable, then - invoke DS9 with a number of command line options or use xpa - from a shell script as a batch processor. Example:<br> - </p> - <p><tt>% export DISPLAY=:1</tt><tt><br> - </tt><tt>% Xvfb :1 -screen 0 1024x768x16 &</tt><tt><br> - </tt><tt>% ds9 -file cmap.fits -zoom to fit -cmap b -grid - skyformat degrees -grid yes -regions ../EMS-names.reg - -saveimage png mytest.png -exit</tt><br> - </p> - <p><b>When I start DS9, I get the following error message:</b></p> - <tt>_X11TransSocketINETConnect: Can't get address for - foo.bar.edu </tt><br> - <tt>couldn't connect to display "foo.bar.edu:0.0"</tt> <br> - <p>DS9 is unable to determine a valid X11 Display server, - because of a number of reasons. Most often this is seen when - you have a laptop configured for a network, but is not - physically connected. You need to set the DISPLAY environment - variable to :0.0 </p> - <blockquote><tt>$ xhost + </tt><br> - <tt>$ set DISPLAY=:0.0 </tt><br> - <tt>$ export DISPLAY </tt><br> - </blockquote> - <p><b>Under Solaris, when I start DS9, my twm window manager - crashes!</b></p> - <p>TWM distributed with X11R5 had a major bug, that was - corrected around 1996. DS9 will trigger this bug, and will - cause TWM to crash. If you are running Solaris, and have X11R5 - installed, be sure that /usr/openwin/bin is in your path - before X11R5/bin. This will insure that you are running the - correct version of TWM . </p> - <p><b>When I run ds9 with the tvtwm window manager, sometimes - the open file dialog box does not appear?</b> </p> - <p>If you are running tvtwm, and you are currently viewing a - virtual screen other than the first, when you open a file, the - dialog box will appear in the first virtual screen, not your - current. This is a bug with tvtwm and not ds9.</p> - </blockquote> - <blockquote> - <p> </p> - </blockquote> - </blockquote> - <blockquote> - <p><b><a name="IRAF"></a>IRAF</b></p> - </blockquote> - <blockquote> - <blockquote> - <blockquote> - <blockquote> </blockquote> - </blockquote> - <p><b>I can't use more than 9 frames with the IMEXAMINE task?</b><br> - </p> - <p>The task <tt>IMEXAMINE</tt> can not be used with frame - numbers greater than 9.</p> - <p><b>Can I display from IRAF to DS9 running under Windows or - MacOSX?</b> </p> - <p>Yes, DS9 for Windows and MacOSX is also a fully functional - IRAF display server. To direct image output from IRAF to DS9 - running under Windows or MacOSX, use the IMTDEV environment - variable. For example, if the machine is named 'foo.bar.edu', - define IMTDEV to the follow value before entering IRAF. </p> - <blockquote><tt>$ setenv IMTDEV inet:5137:foo.bar.edu </tt><br> - <tt>$ cl </tt><br> - <tt>cl> display dev$pix</tt><br> - </blockquote> - <blockquote> - <blockquote> </blockquote> - </blockquote> - <p><b>I'm having problems with </b><b>mscred task </b><b>msczero?</b></p> - DS9 now supports IRAF's new IIS image display protocol. However, - there is one minor problem with the <b>mscred</b> task <b>msczero.</b> - Before using <b>msczero</b>, issue the following command in the - cl:<br> - <br> - <tt>cl> set disable_wcs_maps=""<br> - cl> flpr</tt><br> - <p><b>I find that there is a frustrating delay in performing - operations on images displayed from IRAF - there's a wait of - a second or two before an image is (re)displayed, whereas <i>saoimage</i> - reacts virtually instantly for the same type of operation. - This makes running imexamine on a batch of images a pain, - and using the mouse to change color gamma/bias to desired - values basically impossible.</b> </p> - <p>DS9 and <i>saoimage</i> are similar in speed when working - with IRAF. In fact, DS9 uses the same code to interface - with IRAF as saoimage and ximtool. The only difference - is that DS9 is double buffered, whereas, <i>saoimage</i> and - <i>ximtool</i> only use a single buffer. So with <i>saoimage</i> - and <i>ximtool</i>, you see incremental progress, where - DS9 will render the image all at one time. However, the - overall time to finish rendering should almost be the - same. </p> - <p>DS9 runs in both 8 bit and 24 bit environments, but <i>saoimage</i> - is restricted to 8 bit. If you are running DS9 and <i>saoimage</i> - at the same time, then you must be in 8 bit mode. You should - not see any delay in changing the color bias/contrast - between the two. </p> - <p>However, if you are running DS9 in 24 bit mode, then you will - see slower performance in changing the bias/contrast, as - compared to 8 bit mode. Instead of changing a color look - up table, as in 8 bit mode, DS9 has to update every - pixel on the screen. If your cpu speed is slow, you can - select the Edit:Preferences:True Colorbar to tell DS9 - not to update the entire screen, only a part of the - screen. This should only be needed if your machine is - slower than 200 MHz. Again <i>saoimage</i> does not - even run in 24 bit mode, so there are no comparisons. </p> - <p><b>I try to display an image from IRAF and I get the - following error message:</b></p> - <p><tt>Cannot open device (node!imtool,,512,512)</tt></p> - <p> </p> - <p>DS9 works the same way as <tt>ximtool,</tt> <tt>saoimage,</tt> - and <tt>saotng.</tt> No special scripts should be - needed. If you have one of the above currently working, DS9 - should work <i>out of the box</i>. </p> - <p>IRAF can use one of three methods to communicate with DS9: - fifo, socket, and unix domain name. The DS9 defaults - are:</p> - <blockquote><tt>fifo /dev/imt1</tt> <br> - <tt>port 5137</tt> <br> - <tt>unix /tmp/.IMT%d</tt> </blockquote> - <p>If your IRAF configuration is set up different (i.e., a - different port number, or via a fifo), you need to tell - DS9 how to communicate with iraf. DS9 uses the same - command line options as XIMTOOL: </p> - <blockquote><tt>-fifo </tt> <br> - <tt> -fifo_only </tt><br> - <tt> -inet_only </tt> <br> - <tt> -port </tt> <br> - <tt> -port_only </tt> <br> - <tt> -unix </tt> <br> - <tt> -unix_only </tt> </blockquote> - </blockquote> - </blockquote> - <blockquote> </blockquote> - <blockquote> - <blockquote> - <p><b>I try to display an image, I see something, but it's - corrupted and I get multiple error messages from DS9...</b></p> - <p><b> </b>An IRAF image server (<i>ximtool</i>, <i>saoimage</i>, - DS9, etc...) uses a configuration file to specify the - number of available buffers and their sizes. What actually - passes from IRAF is not the buffer size, but an index - number into this file. </p> - <p>So when an image server starts (DS9), it will attempt to - locate this file as $HOME/.imtoolrc and - /usr/local/lib/imtoolrc. If not found, it will look for - shell environment variables IMTOOLRC and imtoolrc, that - contains the name of the configuration file. </p> - <p>If no configuration file is found, DS9 will assume the - following default configuration: </p> - <blockquote><tt> 1 2 512 512 # - imt1|imt512 </tt><br> - <tt> 2 2 800 800 # imt2|imt800 </tt><br> - <tt> 3 2 1024 1024 # imt3|imt1024 </tt><br> - <tt> 4 1 1600 1600 # imt4|imt1600 </tt><br> - <tt> 5 1 2048 2048 # imt5|imt2048 </tt><br> - <tt> 6 1 4096 4096 # imt6|imt4096 </tt><br> - <tt> 7 1 8192 8192 # imt7|imt8192 </tt><br> - <tt> 8 1 1024 4096 # imt8|imt1x4 </tt><br> - <tt> 9 2 1144 880 # imt9|imtfs full - screen (1152x900 minus frame) </tt><br> - <tt>10 2 1144 764 # imt10|imtfs35 full - screen at 35mm film aspect ratio </tt><br> - <tt>11 2 128 128 # imt11|imt128 </tt><br> - <tt>12 2 256 256 # imt12|imt256 </tt><br> - <tt>13 2 128 1056 # imt13|imttall128 tall - & narrow for spectro. </tt><br> - <tt>14 2 256 1056 # imt14|imttall256 tall - & wider for spectro. </tt><br> - <tt>15 2 1056 128 # imt15|imtwide128 wide - & thin for spectro. </tt><br> - <tt>16 2 1056 256 # imt16|imtwide256 wide - & fatter for spectro. </tt><br> - <tt>17 2 1008 648 # imt17|imtssy Solitaire - fmt w/ imtool border </tt><br> - <tt>18 2 1024 680 # imt18|imtssn Solitaire - fmt w/out imtool border </tt><br> - <tt>19 1 4096 1024 # imt19|imt4x1</tt><br> - </blockquote> - <p>If on the other hand, IRAF assumes a different buffer size, - the image will appear corrupted and DS9 may issue a number of - error messages. </p> - <p>Another problem is that this file must be in sync with - dev$graphcap. If your system administrator has made - changes to graphcap, they must also be implemented in - imtoolrc. </p> - <p>Here is a note from NOAO: </p> - <blockquote> - <p><tt>The messages means that there is no - /usr/local/lib/imtoolrc file </tt><tt>on the machine. - This is created as a symlink to dev$imtoolrc by the </tt><tt>iraf - - - - - - - install script but only if the /usr/local/lib dir already - exists on the </tt><tt>machine. The fix is the create the - dir and rerun the install script or </tt><tt>else make - the link by hand. Users can also just copy - dev$imtoolrc </tt><tt>to $HOME/.imtoolrc and restart the - server to also workaround it. Note </tt><tt>that an - existing .imtoolrc might define old frame buffer configs - which </tt><tt>might confuse things, so if the system - file exists check for a private </tt><tt>copy screwing - things up. </tt></p> - </blockquote> - </blockquote> - </blockquote> - <blockquote> - <blockquote> - <p><b>Where do I find this .imtoolrc file?</b> </p> - <p>Again, here a note from NOAO concerning this issue: </p> - <blockquote> - <p><tt>In a smooth installation the imtoolrc file is installed - as a </tt><tt>/usr/local/lib/imtoolrc symlink pointing to - the dev$imtoolrc file in the </tt><tt>iraf system. - This is normally what's used but XImtool (and DS9?) also </tt><tt>allow - - - - - - - a $HOME/.imtoolrc and IMTOOLRC environment variable - defining the </tt><tt>path as fallbacks. There are - several practical problems with this: for </tt><tt>some - - - - - - - reason (I'm trying to fix) the imtoolrc link won't be - created if </tt><tt>the /usr/local/lib directory doesn't - exist when the install script is </tt><tt>run on the - machine, even though it's run as root and the file can be - </tt><tt>directory easily. On PC-IRAF systems there is - also a typo in the install </tt><tt>script (extra logical - or at line 515) which causes it to exit before </tt><tt>the - - - - - - - display setup is run (i.e. no /dev fifos or imtoolrc). If - users don't </tt><tt>catch this or see it in the README - file they'll think everything went </tt><tt>fine. Lastly, - the local iraf admin might not have run the install script - </tt><tt>on the local iraf NFS client machine at all.</tt></p> - </blockquote> - </blockquote> - </blockquote> - <blockquote> - <blockquote> - <p><b>When I display an image from IRAF, the SCALE menu option - is not active, Why?</b> </p> - <p>When you display an image from IRAF into DS9, IRAF actually - does the color scale distribution. In Display, use the - ztrans and z1,z2 parameters to set the upper/lower bounds and - distribution. You can also use the zscale parameter to auto - determine z1,z2.Here are the DISPLAY parameters in question: </p> - <blockquote><tt>ztrans=[linear|log|none|user] </tt><br> - <tt>z1=min </tt><br> - <tt>z2=max </tt><br> - <tt>zscale=[yes|no]</tt></blockquote> - <p>What actually is sent from IRAF to DS9 is one byte per pixel, - values 0-200, which already has applied both the upper - and lower clipping bounds and the distribution. So this is - why, the SCALE menu is disabled in DS9 when it receives a - image from IRAF.</p> - </blockquote> - </blockquote> - <blockquote> - <p> <b><a name="Coordinates"></a>Coordinates</b></p> - </blockquote> - <blockquote> - <blockquote> - <p><b>Why don't I see PHYSICAL/WCS/WCSA...WCSZ coordinates - displayed when I load my image?</b></p> - <p>DS9 supports the following coordinate systems: </p> - <blockquote><tt>WCS Sky coords (fk4,fk5,icrs,galactic,ecliptic) - <br> - </tt><tt>WCS Linear coords <br> - </tt><tt>Image (also known as Logical) <br> - </tt><tt>Physical (also known as CCD)<br> - Detector<br> - Amplifier </tt><br> - </blockquote> - <p>DS9 uses the following FITS keywords in the header to define - a coordinate system: </p> - </blockquote> - <center> - <table nosave="" width="75%" cellpadding="4" border="1"> - <tbody> - <tr> - <td><b>Coordinate System</b></td> - <td><b>Keyword Values</b></td> - </tr> - <tr nosave=""> - <td nosave=""><tt>WCS / WCSA...WCSZ</tt></td> - <td><tt>CRVAL,CRPIX,CRDELT,CD... (for images) <br> - TCRVL,TCRPX,TCDLT,... (for tables)</tt></td> - </tr> - <tr> - <td><tt>Image</tt></td> - <td><tt>none required</tt></td> - </tr> - <tr> - <td><tt>Physical</tt></td> - <td><tt>WCSNAMEP='PHYSICAL' or LTMx_x/LTVx</tt></td> - </tr> - <tr> - <td valign="top"><tt>Detector</tt><br> - </td> - <td valign="top"><tt>DTMx_x/DTVx</tt><br> - </td> - </tr> - <tr> - <td valign="top"><tt>Amplifier</tt><br> - </td> - <td valign="top"><tt>ATMx_x/ATVx</tt><br> - </td> - </tr> - </tbody> - </table> - </center> - <blockquote> - <p>If the required keywords are not present, values for those - coordinates are not displayed. </p> - <p>Note: For PHYSICAL, DS9 will first look for an alternative - WCS with WCSNAMEx='PHYSICAL'. If not found, DS9 will then look - for the LTMx_x LTVx keywords.</p> - </blockquote> - </blockquote> - <blockquote> - <p> <b><a name="Regions"></a>Regions</b></p> - <blockquote> - <p><b>How do I indicate distance on my printed images?</b> - </p> - <p>You have two choices, the RULER region and the LINE region. - The ruler region is mainly used for interactive measurements. - For printed output, use the LINE region to create a distance - indicator. In the line region dialog, there is a read-only - entry that indicates the length in pixels, degrees, arcmin, or - arcsec. Edit to the desired distance and enter the desired - label, including ' or ", in the region text labile entry. You - have the option of arrows at each end of the line. </p> - </blockquote> - </blockquote> - <blockquote> - <p> <b><a name="Printing"></a>Printing</b></p> - <blockquote> - <p><b>I can make some wonderful color images in DS9 and save - them as postscript files that look great, but often when I - print them they appear washed out or very different than - they do on the screen. My question then is what, if - anything, can I do about this?</b> </p> - <p>The problem is that you create an image on a display, which - is the product of RGB colors (red, green, and blue) and - print the image on a printer, which is the product of - CMYK colors (cyan, yellow, magenta, and black). Furthermore, - every monitor is different in how it will display a - certain color, and every printing technology is - different in how well it will reproduce that color. And - finally, the translation between RGB and CMYK is not - symmetric, i.e. its not possible to translate some - colors back and forth. </p> - <p>It's possible to calibrate your monitor and your printer, to - create a translation matrix, to correct for problems - outlined above (in the Macintosh world, this is what - ColorSync does). The idea is to <i>apply</i> a gamma - correction to the output of DS9, so that it will print - much more in line with what you expect. To do this you'd - need special software and hardware, and its only valid - for your monitor and your printer. </p> - <p>In summary, its not worth it. Especially in the case of - publication, such as ApJ, where you have no idea on what - printing technology will be used to reproduce your - image. So the only control you have is to calibrate your - monitor and to hope for the best. </p> - <p>However, there are some <i>rules of thumb </i>that might - help. First, printers have a very hard time with <i>blues</i> - and <i>purples</i>, as they tend to be washed out. Either - avoid these colors, or over compensate these colors. </p> - <p>ApJ has a good idea in that you send in both an electronic - version and a hard copy of your color image. That way, they - can manually adjust the printers to try to match your - output.</p> - <p><i>NOTE: Even though ApJ requests images in CMYK, we - recommend RGB. From personal experience, if you send RGB, - the printed results will be closer to the original.</i></p> - <p><b>We used DS9 to generate 300 dpi CMYK eps figures, as per - the ApJ specifications, but the color scheme on our - proofs is wrong. In the proofs, the violet is washed - out and looks similar to the black, and the blue is not - nearly as intense.</b></p> - <p><b> </b>There are two issues here: first, color - printers are notorious for failure to reproduce blues and - purples correctly. Second, not all colors in RGB space - can be reproduced correctly in CMYK space, blues being the - prime example. Below is an excerpt from an industry pamphlet:</p> - <blockquote> - <p><tt>Be aware that it is possible to see colors in RGB that - you can't make with CMYK. They are said to be "out of the - CMYK color gamut". What happens is that the RGB-to-CMYK - translator just gets as close as possible to the - appearance of the original and that's as good as it can - be. It's something that everyone in the industry puts up - with. So it's best to select any colors you use for fonts - or other design elements in your layout using CMYK - definitions instead of RGB. That way, you will have a - better idea of how they will appear in your printed piece. - Here's a common example: many programs translate the 100% - Blue in RGB into a somewhat purple-looking color in CMYK. - We recommend a CMYK value of 100-65-0-0 to get a nice - clean blue.<font size="-1"><br> - </font></tt></p> - </blockquote> - <p>For this reason, you may wish to use the RGB color space or - colormaps without deep blues and purples, such as <tt>BB</tt> - or <tt>Heat.</tt></p> - </blockquote> - </blockquote> - <blockquote> - <p> <b><a name="XPA"></a>XPA</b></p> - <blockquote> - <p><b>How can I use XPA to display from a client machine to DS9 - on a server machine?<br> - </b></p> - <p>Assuming you have direct IP reachability between the machines - (i.e. one host can successfully connect() to the other), XPA - does allow you to have an XPA-enabled server like DS9 on one - machine and a client on another. To make this work, you need - to do two things (let's assume DS9 is running on a machine - called "server_host" and you want to send xpa commands from - "client_host"):<br> - </p> - <ol> - <li>The XPA server program (i.e. DS9) must allow the client - host to send XPA commands. Access can be permitted in one of - two ways:<br> - <ol style="list-style-type: lower-alpha;"> - <li>Send the XPA server an acl request by running xpaset - on the same host on which the server is running (i.e. on - the server_host):<br> - <br> - <span style="font-family: monospace;">% xpaset -p ds9 - -acl client_host +<br> - <br> - </span></li> - <li>For more permanent access, add permissions in - ~acls.xpa:<br> - <br> - <span style="font-family: monospace;">% cat > - ~/acls.xpa</span><br style="font-family: monospace;"> - <span style="font-family: monospace;">DS9:ds9 - client_host +<br> - </span><br> - You can check the acls for an XPA server using xpaget: <br> - <br> - <span style="font-family: monospace;">% xpaget ds9 -acl<br> - </span><br> - </li> - </ol> - </li> - <li>On the client side, the client needs to communicate with - the xpansname server program on the server machine to find - the XPA server communication info. This also can be done in - two ways:<br> - <ol style="list-style-type: lower-alpha;"> - <li>use the -i [host] switch to override <span - style="font-family: monospace;">XPA_NSINET</span> for - this execution (The default port is 14285):<br> - <span style="font-family: monospace;"><br> - % xpaget -i 'server_host:14285<span - style="font-family: monospace;">' ds9</span></span><br> - <br> - </li> - <li>Set the <span style="font-family: monospace;">XPA_NSINET</span> - variable for more permanent selection of xpans on the - server host:<br> - <br> - <span style="font-family: monospace;">% setenv - XPA_NSINET 'server_host:14285'</span><br> - </li> - </ol> - </li> - </ol> - <p>Once these two setup steps are performed, you should be able - to send commands to DS9 and receive data from DS9. You can - look at the <a - href="http://hea-www.harvard.edu/saord/xpa/acl.html">xpaacl - man page</a> for more information.</p> - <p><b>I have a laptop, that most of the time, is connected to a - network. DS9 runs fine. However, when I'm not connected to a - network and I start DS9, it hangs. What's going on?</b></p> - <p> DS9 uses XPA for interprocess communication. When DS9 - starts, XPA initializes itself. XPA uses either IP sockets or - UNIX sockets, based if your machine is configured to connect - to the internet. In the case where your machine is configured - for the internet, but you are not currently connected, XPA - gets very confused. So, you can define a shell variable, - XPA_METHOD, that tells XPA which method to use. </p> - <p>The following is from the XPA documentation: </p> - <blockquote> - <p><tt>Determines the socket connection method used by this - session of XPA. The choices are: inet (to use INET or - Internet-based sockets) and local (unix) (to use UNIX - sockets). The default is INET. Using the inet method will - allow access from other machines (subject to access - controls) but using local will not. Local is most useful - for private access and when the machine in question is not - connected to the Internet</tt></p> - </blockquote> - <p>More information is available on XPA shell variables at: <a - href="http://hea-www.harvard.edu/RD/xpa/env.html">The XPA - Environment</a><br> - </p> - </blockquote> - </blockquote> - <blockquote> - <blockquote> - <p> </p> - </blockquote> - </blockquote> - <blockquote> - <p><b><a name="VO"></a>VO</b></p> - <blockquote> - <p><b>I can't connect to any of the virtual observatories. What - do I do now?</b></p> - <p>The DS9 help facility now contains a tutorial on how to - configure DS9 to by pass network firewalls. See <a - href="ref/vo.html">Virtual Observatory Reference</a> for - more information.</p> - </blockquote> - </blockquote> - </body> +<head> +<meta name="generator" content= +"HTML Tidy for Mac OS X (vers 31 October 2006 - Apple Inc. build 15.18.1), see www.w3.org"> +<meta http-equiv="Content-Type" content= +"text/html; charset=us-ascii"> +<meta name="GENERATOR" content= +"Mozilla/4.78 [en] (X11; U; Linux 2.4.7-10 i686) [Netscape]"> +<title>DS9 FAQ</title> +</head> +<body vlink="#551A8B" text="#000000" link="#0000EE" bgcolor= +"#FFFFFF" alink="#FF0000"> +<h3><img alt="" src="sun.gif" width="100" height="98" align= +"middle"> SAOImageDS9 FAQ</h3> +<blockquote> +<p>This FAQ is a new, on going project, and it is far from being +complete. But as common questions on DS9 are received, the FAQ will +be updated.</p> +<p><b>Contents</b></p> +<blockquote><a href="#Copyright">Copyright</a><br> +<a href="#General">General</a><br> +<a href="#Fonts">Fonts</a><br> +<a href="faq.html#Linux">Linux</a><br> +<a href="faq.html#Windows">Windows</a><br> +<a href="#MacOSX">MacOSX</a><br> +<a href="faq.html#X11">X11</a><br> +<a href="#IRAF">IRAF</a><br> +<a href="#Coordinates">Coordinates</a><br> +<a href="#Regions">Regions</a><br> +<a href="#Printing">Printing</a><br> +<a href="#XPA">XPA</a><br> +<a href="#VO">VO</a><br></blockquote> +</blockquote> +<blockquote> +<p><b><a name="Copyright" id="Copyright"></a>Copyright</b></p> +<blockquote> +<p>DS9 is composed of approximately 20 open source packages, all of +which are distributed under their own open source license +agreements, usually GPL, LGPL, or BSD. In addition, several open +source packages have been developed here at the Smithsonian +Astrophysical Observatory, Cambridge, MA, USA and are distributed +under the terms of the GNU General Public License as published by +the Free Software Foundation. As long as you continue to adhere to +the provisions of the licenses, you are free to distribute DS9 +along with your software.</p> +<p>The <a href="http://www.gnu.org/copyleft/gpl.html">GNU site</a> +contains an excellent FAQ on the the dos and donts of GPL.</p> +</blockquote> +<p><b><a name="General" id="General"></a>General</b></p> +<blockquote> +<p><b>The web browser, catalog tool, image server, and other +Analysis functions don't appear to work. Whats going +on?<br></b></p> +<p>For a number of the Analysis functions, DS9 requires temporary +disk space to download and store data. By default, this directory +is defined by the TMP or TEMP environment variable. This is usually +defined as <tt>/tmp</tt> for Linux and MacOSX users. For Windows +users, this will vary, depending on which version of Windows you +have. In any case, if the temp directory is not writable, or you +have specified an invalid directory in the preferences, these +functions will fail with a variety of error messages.<br></p> +<p><b>My system admin stripped the DS9 binary and now DS9 fails to +start with the following error message:</b></p> +<p><tt>Application initialization failed: Can't find a usable +tk.tcl in the following directories...</tt></p> +<p>DS9 is based on tcl/tk which is a scripting language which +requires many support files. To create a stand alone application, +we <i>fool</i> tcl/tk into thinking that it has a valid +installation. To do this, DS9 is really an application, along with +an zip archive attached. The first thing DS9 does is to create a +virtual file system in memory and unpack that archive into memory. +The application DS9 is already stripped of debugging symbols when +built.</p> +<p>It appears that the <tt>strip</tt> command is <i>stripping</i> +part of the archive, hence DS9 is unable to un-compress it. In +summary, don't <tt>strip</tt> the DS9 binary and everything works +fine.</p> +<p><b>When I open my FITS image, all I see is 'white'. Yet +everything, including the color bar seems to work?</b></p> +<p>New with version 2.1, is support for the DATASEC keyword. This +keyword specifies what portion of the image is valid data, for +calculating min / max and for displaying. This is very important +for images created from CCDs with over scan and bias strips. By +default, this support is enabled. However, a number of fits images +with this keyword, have invalid values. Therefor, when DS9 opens +the image, it finds no valid data to display. To correct this +problem, either disable DATASEC support, via the Scale menu, or +correct the the value of DATASEC in the fits header. You can also +change the default behavior by disabling DATASEC from the +preferences menu.<br></p> +</blockquote> +<p><b><a name="Fonts" id="Fonts"></a>Fonts</b></p> +<blockquote> +<p><b>Where is the Symbol Font? How do I enter special characters +into an entry dialog?</b></p> +<p>The concept of a separate <tt>SYMBOL</tt> font is no longer +implemented with the latest OS font and scripting support, +especially with scalable anti-alias fonts such as Xft for Linux. +Most newer fonts (if not all) now have greek characters as part of +the font. The greek chars start at unicode \u0391 for 'A' and +\u03b1 for 'a'. Each OS has a tool used to build and copy a string +of characters. Then use the Edit:Paste menu of DS9 to insert the +character string.</p> +<p>Linux- Gnome: <b>gucharmap<br></b> Linux- KDE: +<b>kcharselect<br></b> MacOSX: <b>Character Viewer</b> (Select +<tt>Edit:Special Characters</tt>) Now click and drag the characters +to a terminal window. Then select the string and select +<tt>Edit:Copy</tt>.<br> +Windows: <b>Character Map</b> (from <tt>Start</tt> button, select +<tt>All Programs</tt>, <tt>Accessories</tt>, <tt>System Tools</tt> +and then <tt>Character Map</tt>)<br></p> +</blockquote> +<p><b><a name="Linux" id="Linux"></a>Linux</b></p> +<blockquote> +<p><b>My /tmp directory is mounted -noexec and bin table filtering +does not work.</b></p> +<p>Set the environment variable FILTER_TMPDIR to a directory that +is both writable and can execute.<br></p> +<p><b>I have Red Hat 7, and I'm running KDE. The magnifier keeps +going blank after a few seconds, what's going on?</b></p> +<p>The problem was in KDE. If the user has decided to hide the +panel taskbar and sets a delay time for when it appears if +the mouse is moved to the panel location, then it appears +that KDE creates mouse events that fool DS9 into thinking the +mouse is outside and it blanks the magnifier. By turning off +the hide panel, the effect goes away. The alternative is to +update to KDE2.1Beta where this method of dealing with the +hidden panel is not used and all is well, as it was for +KDE</p> +<p><b>I have FreeBSD. When I run ds9, I get the following +error:</b> <tt> <b>ELF binary type "0" not known</b></tt> +<b>Whats going on?</b></p> +<p>The solution was to use the <b><tt>brandelf</tt></b> utility on +the file to ensure that the machine understood that it was a +Linux program.</p> +<p><tt>% brandelf -t Linux (file name)<br></tt></p> +</blockquote> +<p><b><a name="Windows" id="Windows"></a>Windows</b></p> +<blockquote> +<p><b>When I do Save Image, I get the same result (and this is true +for either .gif, .jpeg, .tiff, .png and .ppm) : it saves only a +stripe at the top of my image.<br></b></p> +<p>This problem seems to be caused by running DS9 in Windows XP +compatibility mode. Please un-check the compatibility option in the +properties dialog.<br></p> +<p><b>How can I open a FITS file with an extension name?</b></p> +<p>By default, the windows port of DS9 uses the Windows standard +dialog box to open and save files. This can be a problem in that +the native Windows dialog will not allow extensions to the file +name, such as <tt>foo.fits[2]</tt>. You must use the Unix like +standard dialogs to be able to specify an extension. Select +<tt>Edit->Preferences->General:Dialogbox</tt> to change the +default standard dialog.</p> +<p><b>Every time I create an auxiliary window in ds9, such as a +Pixel Table, or Analysis Plot, it will retreat behind the main ds9 +window. Then, when I bring the auxiliary window to the front and +move the mouse out of it, it automatically goes behind the main ds9 +window again. What can I do to fix things so that the auxiliary +window stays on top of the ds9 window?</b></p> +<p>To fix things so that the auxiliary window stays on top of the +ds9 window, do the following:</p> +<blockquote> +<p><tt>Go to the icon task bar at the bottom of the screen.</tt> +<tt>Bring the auxiliary window to the front by clicking on its icon +in the icon task bar.</tt> <tt>While the mouse still is on the aux +window icon, press the mouse button, and keeping it pressed, move +the mouse off the task bar.</tt> <tt>Release the mouse while off +the task bar.</tt> <tt>The auxiliary window will now stay on top of +the main ds9 window.</tt></p> +</blockquote> +</blockquote> +<p><b><a name="MacOSX" id="MacOSX"></a>MacOSX</b><br></p> +<blockquote> +<p><b>I can't invoke the 'Save Image' function from the MacOSX X11 +version. I get an error message "An error has occurred while +creating the image. Please make sure entire image is visible on +screen."<br></b></p> +Up until MacOSX 10.8 (Mountain Lion), Apple provided their own +version of a X11 server. At first, it was based on XFree86 +(X11R6.6) and available with versions up to MacOSX 10.4. Later with +MacOSX versions 10.5 to 10.7, the Apple's X11 server was based upon +X.org (X11R7.2).<br> +<br> +The Apple version of X11 server for MacOSX 10.5 to 10.7 contains a +bug which fails if you invoke certain X11 calls on a window if its +location is not at 0,0 on the screen. Hence, within DS9, if you +'Save Image' and your window is not exactly in the upper left +corner, it will fail.<br> +<br> +Again, this only affects users of MacOSX 10.5 to 10.7.<br> +<br> +Starting with MacOSX 10.8, Apple no longer provides a X11 window +server. The user must go to the XQuartz site and download/install +directly. The current version is 2.7.3.<br> +<p><b>When I invoke DS9 MacOSX Aqua from the command line, I get +weird errors such as<tt>:</tt></b></p> +<blockquote> +<p><tt>The document "foo.fits" could not be opened. SAOImage DS9 +cannot open files in the "Flexible Image Transport System" +format.</tt></p> +</blockquote> +<p>When opening MacOSX Aqua from the command line, it is better to +use the <tt>OPEN</tt> application as opposed to specifying the +binary directly. The <tt>OPEN</tt> application sets up the +environment just as it is when a user double clicks.</p> +<tt># good</tt><br> +<tt>% open /Applications/SAOImage\ DS9.app foo.fits<br> +<br> +# bad<br> +% /Applications/SAOImage\ DS9.app/Contents/MacOS/ds9 +bar.fits</tt><br> +<p><b>How can I open a FITS file with an extension name?</b></p> +<p>By default, DS9 MacOSX Aqua uses the MacOSX standard dialog box +to open and save files. This can be a problem in that the native +MacOSX dialog will not allow extensions to the file name, such as +<tt>foo.fits[2]</tt>. You must use the Unix like standard dialogs +to be able to specify an extension. Select +<tt>Edit->Preferences->General</tt> to change the default +standard dialog.</p> +<p><b>How do I set my PATH environment variable under MacOSX for +use with external analysis programs, such as funtools?<br></b></p> +<p>When you double click on a MacOSX application, it does not parse +any shell startup files, such as ~/.profile. Instead, the +environment is defined using a special environment file, +<tt>.MacOSX/environment.plist</tt>. This file can be created with +the MacOSX utility +<tt>/Developer/Applications/PropertyListEditor.app.</tt> For +further information, please click <a href= +"http://developer.apple.com/qa/qa2001/qa1067.html">here</a>.<br></p> +</blockquote> +<p><b><a name="X11" id="X11"></a>X11</b><br></p> +<blockquote> +<p><b>Is it possible to work in batch mode without a physical +display?<br></b></p> +<p>DS9 is written as an interactive, window client program, and as +a result, does require a window server to be available for +rendering (X11, Windows, or MacOSX).<br> +<br> +Therefore, using DS9 as a batch process can be cumbersome. We +recommend using <tt>xvfb</tt> under X11. Just set up a virtual +display buffer, reset your DISPLAY variable, then invoke DS9 with a +number of command line options or use xpa from a shell script as a +batch processor. Example:<br></p> +<p><tt>% export DISPLAY=:1</tt><tt><br></tt> <tt>% Xvfb :1 -screen +0 1024x768x16 &</tt><tt><br></tt> <tt>% ds9 -file cmap.fits +-zoom to fit -cmap b -grid skyformat degrees -grid yes -regions +../EMS-names.reg -saveimage png mytest.png -exit</tt><br></p> +<p><b>When I start DS9, I get the following error message:</b></p> +<tt>_X11TransSocketINETConnect: Can't get address for +foo.bar.edu</tt><br> +<tt>couldn't connect to display "foo.bar.edu:0.0"</tt> <br> +<p>DS9 is unable to determine a valid X11 Display server, because +of a number of reasons. Most often this is seen when you have a +laptop configured for a network, but is not physically connected. +You need to set the DISPLAY environment variable to :0.0</p> +<blockquote><tt>$ xhost +</tt><br> +<tt>$ set DISPLAY=:0.0</tt><br> +<tt>$ export DISPLAY</tt><br></blockquote> +<p><b>Under Solaris, when I start DS9, my twm window manager +crashes!</b></p> +<p>TWM distributed with X11R5 had a major bug, that was corrected +around 1996. DS9 will trigger this bug, and will cause TWM to +crash. If you are running Solaris, and have X11R5 installed, be +sure that /usr/openwin/bin is in your path before X11R5/bin. This +will insure that you are running the correct version of TWM .</p> +<p><b>When I run ds9 with the tvtwm window manager, sometimes the +open file dialog box does not appear?</b></p> +<p>If you are running tvtwm, and you are currently viewing a +virtual screen other than the first, when you open a file, the +dialog box will appear in the first virtual screen, not your +current. This is a bug with tvtwm and not ds9.</p> +</blockquote> +</blockquote> +<blockquote> +<p><b><a name="IRAF" id="IRAF"></a>IRAF</b></p> +</blockquote> +<blockquote> +<blockquote> +<p><b>I can't use more than 9 frames with the IMEXAMINE +task?</b><br></p> +<p>The task <tt>IMEXAMINE</tt> can not be used with frame numbers +greater than 9.</p> +<p><b>Can I display from IRAF to DS9 running under Windows or +MacOSX?</b></p> +<p>Yes, DS9 for Windows and MacOSX is also a fully functional IRAF +display server. To direct image output from IRAF to DS9 running +under Windows or MacOSX, use the IMTDEV environment variable. For +example, if the machine is named 'foo.bar.edu', define IMTDEV to +the follow value before entering IRAF.</p> +<blockquote><tt>$ setenv IMTDEV inet:5137:foo.bar.edu</tt><br> +<tt>$ cl</tt><br> +<tt>cl> display dev$pix</tt><br></blockquote> +<p><b>I'm having problems with</b> <b>mscred task</b> +<b>msczero?</b></p> +DS9 now supports IRAF's new IIS image display protocol. However, +there is one minor problem with the <b>mscred</b> task +<b>msczero.</b> Before using <b>msczero</b>, issue the following +command in the cl:<br> +<br> +<tt>cl> set disable_wcs_maps=""<br> +cl> flpr</tt><br> +<p><b>I find that there is a frustrating delay in performing +operations on images displayed from IRAF - there's a wait of a +second or two before an image is (re)displayed, whereas +<i>saoimage</i> reacts virtually instantly for the same type of +operation. This makes running imexamine on a batch of images a +pain, and using the mouse to change color gamma/bias to desired +values basically impossible.</b></p> +<p>DS9 and <i>saoimage</i> are similar in speed when working with +IRAF. In fact, DS9 uses the same code to interface with IRAF +as saoimage and ximtool. The only difference is that DS9 is +double buffered, whereas, <i>saoimage</i> and <i>ximtool</i> +only use a single buffer. So with <i>saoimage</i> and +<i>ximtool</i>, you see incremental progress, where DS9 will +render the image all at one time. However, the overall time +to finish rendering should almost be the same.</p> +<p>DS9 runs in both 8 bit and 24 bit environments, but +<i>saoimage</i> is restricted to 8 bit. If you are running DS9 and +<i>saoimage</i> at the same time, then you must be in 8 bit mode. +You should not see any delay in changing the color +bias/contrast between the two.</p> +<p>However, if you are running DS9 in 24 bit mode, then you will +see slower performance in changing the bias/contrast, as +compared to 8 bit mode. Instead of changing a color look up +table, as in 8 bit mode, DS9 has to update every pixel on the +screen. If your cpu speed is slow, you can select the +Edit:Preferences:True Colorbar to tell DS9 not to update the entire +screen, only a part of the screen. This should only be needed +if your machine is slower than 200 MHz. Again <i>saoimage</i> +does not even run in 24 bit mode, so there are no +comparisons.</p> +<p><b>I try to display an image from IRAF and I get the following +error message:</b></p> +<p><tt>Cannot open device (node!imtool,,512,512)</tt></p> +<p>DS9 works the same way as <tt>ximtool,</tt> <tt>saoimage,</tt> +and <tt>saotng.</tt> No special scripts should be needed. If +you have one of the above currently working, DS9 should work +<i>out of the box</i>.</p> +<p>IRAF can use one of three methods to communicate with DS9: fifo, +socket, and unix domain name. The DS9 defaults are:</p> +<blockquote><tt>fifo /dev/imt1</tt><br> +<tt>port 5137</tt><br> +<tt>unix /tmp/.IMT%d</tt></blockquote> +<p>If your IRAF configuration is set up different (i.e., a +different port number, or via a fifo), you need to tell DS9 +how to communicate with iraf. DS9 uses the same command line +options as XIMTOOL:</p> +<blockquote><tt>-fifo</tt><br> +<tt>-fifo_only</tt><br> +<tt>-inet_only</tt><br> +<tt>-port</tt><br> +<tt>-port_only</tt><br> +<tt>-unix</tt><br> +<tt>-unix_only</tt></blockquote> +</blockquote> +</blockquote> +<blockquote> +<blockquote> +<p><b>I try to display an image, I see something, but it's +corrupted and I get multiple error messages from DS9...</b></p> +<p>An IRAF image server (<i>ximtool</i>, <i>saoimage</i>, DS9, +etc...) uses a configuration file to specify the number of +available buffers and their sizes. What actually passes from +IRAF is not the buffer size, but an index number into this +file.</p> +<p>So when an image server starts (DS9), it will attempt to locate +this file as $HOME/.imtoolrc and /usr/local/lib/imtoolrc. If +not found, it will look for shell environment variables +IMTOOLRC and imtoolrc, that contains the name of the configuration +file.</p> +<p>If no configuration file is found, DS9 will assume the following +default configuration:</p> +<blockquote><tt> 1 2 512 512 # +imt1|imt512</tt><br> +<tt> 2 2 800 800 # +imt2|imt800</tt><br> +<tt> 3 2 1024 1024 # imt3|imt1024</tt><br> +<tt> 4 1 1600 1600 # imt4|imt1600</tt><br> +<tt> 5 1 2048 2048 # imt5|imt2048</tt><br> +<tt> 6 1 4096 4096 # imt6|imt4096</tt><br> +<tt> 7 1 8192 8192 # imt7|imt8192</tt><br> +<tt> 8 1 1024 4096 # imt8|imt1x4</tt><br> +<tt> 9 2 1144 880 # imt9|imtfs full screen +(1152x900 minus frame)</tt><br> +<tt>10 2 1144 764 # imt10|imtfs35 full screen at +35mm film aspect ratio</tt><br> +<tt>11 2 128 128 # imt11|imt128</tt><br> +<tt>12 2 256 256 # imt12|imt256</tt><br> +<tt>13 2 128 1056 # imt13|imttall128 tall & +narrow for spectro.</tt><br> +<tt>14 2 256 1056 # imt14|imttall256 tall & +wider for spectro.</tt><br> +<tt>15 2 1056 128 # imt15|imtwide128 wide & +thin for spectro.</tt><br> +<tt>16 2 1056 256 # imt16|imtwide256 wide & +fatter for spectro.</tt><br> +<tt>17 2 1008 648 # imt17|imtssy Solitaire fmt w/ +imtool border</tt><br> +<tt>18 2 1024 680 # imt18|imtssn Solitaire fmt +w/out imtool border</tt><br> +<tt>19 1 4096 1024 # imt19|imt4x1</tt><br></blockquote> +<p>If on the other hand, IRAF assumes a different buffer size, the +image will appear corrupted and DS9 may issue a number of error +messages.</p> +<p>Another problem is that this file must be in sync with +dev$graphcap. If your system administrator has made changes +to graphcap, they must also be implemented in imtoolrc.</p> +<p>Here is a note from NOAO:</p> +<blockquote> +<p><tt>The messages means that there is no /usr/local/lib/imtoolrc +file</tt> <tt>on the machine. This is created as a symlink to +dev$imtoolrc by the</tt> <tt>iraf install script but only if the +/usr/local/lib dir already exists on the</tt> <tt>machine. The fix +is the create the dir and rerun the install script or</tt> <tt>else +make the link by hand. Users can also just copy +dev$imtoolrc</tt> <tt>to $HOME/.imtoolrc and restart the server to +also workaround it. Note</tt> <tt>that an existing .imtoolrc might +define old frame buffer configs which</tt> <tt>might confuse +things, so if the system file exists check for a private</tt> +<tt>copy screwing things up.</tt></p> +</blockquote> +</blockquote> +</blockquote> +<blockquote> +<blockquote> +<p><b>Where do I find this .imtoolrc file?</b></p> +<p>Again, here a note from NOAO concerning this issue:</p> +<blockquote> +<p><tt>In a smooth installation the imtoolrc file is installed as +a</tt> <tt>/usr/local/lib/imtoolrc symlink pointing to the +dev$imtoolrc file in the</tt> <tt>iraf system. This is +normally what's used but XImtool (and DS9?) also</tt> <tt>allow a +$HOME/.imtoolrc and IMTOOLRC environment variable defining the</tt> +<tt>path as fallbacks. There are several practical problems +with this: for</tt> <tt>some reason (I'm trying to fix) +the imtoolrc link won't be created if</tt> <tt>the /usr/local/lib +directory doesn't exist when the install script is</tt> <tt>run on +the machine, even though it's run as root and the file can be</tt> +<tt>directory easily. On PC-IRAF systems there is also a typo +in the install</tt> <tt>script (extra logical or at line 515) which +causes it to exit before</tt> <tt>the display setup is run (i.e. no +/dev fifos or imtoolrc). If users don't</tt> <tt>catch this or see +it in the README file they'll think everything went</tt> <tt>fine. +Lastly, the local iraf admin might not have run the install +script</tt> <tt>on the local iraf NFS client machine at +all.</tt></p> +</blockquote> +</blockquote> +</blockquote> +<blockquote> +<blockquote> +<p><b>When I display an image from IRAF, the SCALE menu option is +not active, Why?</b></p> +<p>When you display an image from IRAF into DS9, IRAF actually does +the color scale distribution. In Display, use the ztrans and +z1,z2 parameters to set the upper/lower bounds and distribution. +You can also use the zscale parameter to auto determine z1,z2.Here +are the DISPLAY parameters in question:</p> +<blockquote><tt>ztrans=[linear|log|none|user]</tt><br> +<tt>z1=min</tt><br> +<tt>z2=max</tt><br> +<tt>zscale=[yes|no]</tt></blockquote> +<p>What actually is sent from IRAF to DS9 is one byte per pixel, +values 0-200, which already has applied both the upper and +lower clipping bounds and the distribution. So this is why, the +SCALE menu is disabled in DS9 when it receives a image from +IRAF.</p> +</blockquote> +</blockquote> +<blockquote> +<p><b><a name="Coordinates" id= +"Coordinates"></a>Coordinates</b></p> +</blockquote> +<blockquote> +<blockquote> +<p><b>Why don't I see PHYSICAL/WCS/WCSA...WCSZ coordinates +displayed when I load my image?</b></p> +<p>DS9 supports the following coordinate systems:</p> +<blockquote><tt>WCS Sky coords +(fk4,fk5,icrs,galactic,ecliptic)<br></tt> <tt>WCS Linear +coords<br></tt> <tt>Image (also known as Logical)<br></tt> +<tt>Physical (also known as CCD)<br> +Detector<br> +Amplifier </tt><br></blockquote> +<p>DS9 uses the following FITS keywords in the header to define a +coordinate system: </p> +</blockquote> +<center> +<table nosave="" width="75%" cellpadding="4" border="1"> +<tbody> +<tr> +<td><b>Coordinate System</b></td> +<td><b>Keyword Values</b></td> +</tr> +<tr nosave=""> +<td nosave=""><tt>WCS / WCSA...WCSZ</tt></td> +<td><tt>CRVAL,CRPIX,CRDELT,CD... (for images)<br> +TCRVL,TCRPX,TCDLT,... (for tables)</tt></td> +</tr> +<tr> +<td><tt>Image</tt></td> +<td><tt>none required</tt></td> +</tr> +<tr> +<td><tt>Physical</tt></td> +<td><tt>WCSNAMEP='PHYSICAL' or LTMx_x/LTVx</tt></td> +</tr> +<tr> +<td valign="top"><tt>Detector</tt><br></td> +<td valign="top"><tt>DTMx_x/DTVx</tt><br></td> +</tr> +<tr> +<td valign="top"><tt>Amplifier</tt><br></td> +<td valign="top"><tt>ATMx_x/ATVx</tt><br></td> +</tr> +</tbody> +</table> +</center> +<blockquote> +<p>If the required keywords are not present, values for those +coordinates are not displayed.</p> +<p>Note: For PHYSICAL, DS9 will first look for an alternative WCS +with WCSNAMEx='PHYSICAL'. If not found, DS9 will then look for the +LTMx_x LTVx keywords.</p> +</blockquote> +</blockquote> +<blockquote> +<p><b><a name="Regions" id="Regions"></a>Regions</b></p> +<blockquote> +<p><b>How do I indicate distance on my printed +images?</b> </p> +<p>You have two choices, the RULER region and the LINE region. The +ruler region is mainly used for interactive measurements. For +printed output, use the LINE region to create a distance indicator. +In the line region dialog, there is a read-only entry that +indicates the length in pixels, degrees, arcmin, or arcsec. Edit to +the desired distance and enter the desired label, including ' or ", +in the region text labile entry. You have the option of arrows at +each end of the line.</p> +</blockquote> +</blockquote> +<blockquote> +<p><b><a name="Printing" id="Printing"></a>Printing</b></p> +<blockquote> +<p><b>I can make some wonderful color images in DS9 and save them +as postscript files that look great, but often when I print them +they appear washed out or very different than they do on the +screen. My question then is what, if anything, can I do about +this?</b></p> +<p>The problem is that you create an image on a display, which is +the product of RGB colors (red, green, and blue) and print +the image on a printer, which is the product of CMYK colors +(cyan, yellow, magenta, and black). Furthermore, every +monitor is different in how it will display a certain color, and +every printing technology is different in how well it will +reproduce that color. And finally, the translation between +RGB and CMYK is not symmetric, i.e. its not possible to +translate some colors back and forth.</p> +<p>It's possible to calibrate your monitor and your printer, to +create a translation matrix, to correct for problems outlined +above (in the Macintosh world, this is what ColorSync does). +The idea is to <i>apply</i> a gamma correction to the output of +DS9, so that it will print much more in line with what you +expect. To do this you'd need special software and hardware, +and its only valid for your monitor and your printer.</p> +<p>In summary, its not worth it. Especially in the case of +publication, such as ApJ, where you have no idea on what +printing technology will be used to reproduce your image. So +the only control you have is to calibrate your monitor and to +hope for the best.</p> +<p>However, there are some <i>rules of thumb</i> that might help. +First, printers have a very hard time with <i>blues</i> and +<i>purples</i>, as they tend to be washed out. Either avoid these +colors, or over compensate these colors. </p> +<p>ApJ has a good idea in that you send in both an electronic +version and a hard copy of your color image. That way, they can +manually adjust the printers to try to match your output.</p> +<p><i>NOTE: Even though ApJ requests images in CMYK, we recommend +RGB. From personal experience, if you send RGB, the printed results +will be closer to the original.</i></p> +<p><b>We used DS9 to generate 300 dpi CMYK eps figures, as per the +ApJ specifications, but the color scheme on our proofs is +wrong. In the proofs, the violet is washed out and looks +similar to the black, and the blue is not nearly as +intense.</b></p> +<p>There are two issues here: first, color printers are +notorious for failure to reproduce blues and purples correctly. +Second, not all colors in RGB space can be reproduced +correctly in CMYK space, blues being the prime example. Below is an +excerpt from an industry pamphlet:</p> +<blockquote> +<p><tt>Be aware that it is possible to see colors in RGB that you +can't make with CMYK. They are said to be "out of the CMYK color +gamut". What happens is that the RGB-to-CMYK translator just gets +as close as possible to the appearance of the original and that's +as good as it can be. It's something that everyone in the industry +puts up with. So it's best to select any colors you use for fonts +or other design elements in your layout using CMYK definitions +instead of RGB. That way, you will have a better idea of how they +will appear in your printed piece. Here's a common example: many +programs translate the 100% Blue in RGB into a somewhat +purple-looking color in CMYK. We recommend a CMYK value of +100-65-0-0 to get a nice clean blue.<font size= +"-1"><br></font></tt></p> +</blockquote> +<p>For this reason, you may wish to use the RGB color space or +colormaps without deep blues and purples, such as <tt>BB</tt> or +<tt>Heat.</tt></p> +</blockquote> +</blockquote> +<blockquote> +<p><b><a name="XPA" id="XPA"></a>XPA</b></p> +<blockquote> +<p><b>How can I use XPA to display from a client machine to DS9 on +a server machine?<br></b></p> +<p>Assuming you have direct IP reachability between the machines +(i.e. one host can successfully connect() to the other), XPA does +allow you to have an XPA-enabled server like DS9 on one machine and +a client on another. To make this work, you need to do two things +(let's assume DS9 is running on a machine called "server_host" and +you want to send xpa commands from "client_host"):<br></p> +<ol> +<li>The XPA server program (i.e. DS9) must allow the client host to +send XPA commands. Access can be permitted in one of two ways:<br> +<ol style="list-style-type: lower-alpha;"> +<li>Send the XPA server an acl request by running xpaset on the +same host on which the server is running (i.e. on the +server_host):<br> +<br> +<span style="font-family: monospace;">% xpaset -p ds9 -acl +client_host +<br> +<br></span></li> +<li>For more permanent access, add permissions in ~acls.xpa:<br> +<br> +<span style="font-family: monospace;">% cat > +~/acls.xpa</span><br style="font-family: monospace;"> +<span style="font-family: monospace;">DS9:ds9 client_host ++<br></span><br> +You can check the acls for an XPA server using xpaget:<br> +<br> +<span style="font-family: monospace;">% xpaget ds9 +-acl<br></span><br></li> +</ol> +</li> +<li>On the client side, the client needs to communicate with the +xpansname server program on the server machine to find the XPA +server communication info. This also can be done in two ways:<br> +<ol style="list-style-type: lower-alpha;"> +<li>use the -i [host] switch to override <span style= +"font-family: monospace;">XPA_NSINET</span> for this execution (The +default port is 14285):<br> +<span style="font-family: monospace;"><br> +% xpaget -i 'server_host:14285<span style= +"font-family: monospace;">' ds9</span></span><br> +<br></li> +<li>Set the <span style="font-family: monospace;">XPA_NSINET</span> +variable for more permanent selection of xpans on the server +host:<br> +<br> +<span style="font-family: monospace;">% setenv XPA_NSINET +'server_host:14285'</span><br></li> +</ol> +</li> +</ol> +<p>Once these two setup steps are performed, you should be able to +send commands to DS9 and receive data from DS9. You can look at the +<a href="http://hea-www.harvard.edu/saord/xpa/acl.html">xpaacl man +page</a> for more information.</p> +<p><b>I have a laptop, that most of the time, is connected to a +network. DS9 runs fine. However, when I'm not connected to a +network and I start DS9, it hangs. What's going on?</b></p> +<p> DS9 uses XPA for interprocess communication. When DS9 +starts, XPA initializes itself. XPA uses either IP sockets or UNIX +sockets, based if your machine is configured to connect to the +internet. In the case where your machine is configured for the +internet, but you are not currently connected, XPA gets very +confused. So, you can define a shell variable, XPA_METHOD, that +tells XPA which method to use.</p> +<p>The following is from the XPA documentation:</p> +<blockquote> +<p><tt>Determines the socket connection method used by this session +of XPA. The choices are: inet (to use INET or Internet-based +sockets) and local (unix) (to use UNIX sockets). The default is +INET. Using the inet method will allow access from other machines +(subject to access controls) but using local will not. Local is +most useful for private access and when the machine in question is +not connected to the Internet</tt></p> +</blockquote> +<p>More information is available on XPA shell variables at: +<a href="http://hea-www.harvard.edu/RD/xpa/env.html">The XPA +Environment</a><br></p> +</blockquote> +</blockquote> +<blockquote> +<p><b><a name="VO" id="VO"></a>VO</b></p> +<blockquote> +<p><b>I can't connect to any of the virtual observatories. What do +I do now?</b></p> +<p>The DS9 help facility now contains a tutorial on how to +configure DS9 to by pass network firewalls. See <a href= +"ref/vo.html">Virtual Observatory Reference</a> for more +information.</p> +</blockquote> +</blockquote> +</body> </html> |